Elastic energy driven polymerization

Reversible strain-promoted DNA polymerization

Molecular strain can be introduced to influence the outcome of chemical reactions. Once a thermodynamic product is formed, however, reversing the course of a strain-promoted reaction is challenging. Here, a reversible, strain-promoted polymerization in cyclic DNA is reported. The use of nonhybridizing, single-stranded spacers as short as a single nucleotide in length can promote DNA cyclization. Molecular strain is generated by duplexing the spacers, leading to ring opening and subsequent polymerization. Then, removal of the strain-generating duplexers triggers depolymerization and cyclic dimer recovery via enthalpy-driven cyclization and entropy-mediated ring contraction. This reversibility is retained even when a protein is conjugated to the DNA strands, and the architecture of the protein assemblies can be modulated between bivalent and polyvalent states. This work underscores the utility of using DNA not only as a programmable ligand for assembly but also as a route to access restorable bonds, thus providing a molecular basis for DNA-based materials with shape-memory, self-healing, and stimuli-responsive properties.

Binding and backbone dynamics of protein under topological constraint: calmodulin as a model system

Herein we present the effect of artificially imposed topological constraint on calmodulin (CaM) backbone dynamics and its molecular recognition behavior. While backbone dynamics of CaM remain largely unperturbed, the thermodynamic profile of CaM binding to the smooth-muscle myosin light-chain kinase (smMLCK) peptide is modulated significantly.

Nucleic Acid Templated Reactions for Chemical Biology

Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging.

DNA-based control of protein activity

DNA has emerged as a highly versatile construction material for nanometer-sized structures and sophisticated molecular machines and circuits. The successful application of nucleic acid based systems greatly relies on their ability to autonomously sense and act on their environment. In this feature article, the development of DNA-based strategies to dynamically control protein activity via oligonucleotide triggers is discussed. Depending on the desired application, protein activity can be controlled by directly conjugating them to an oligonucleotide handle, or expressing them as a fusion protein with DNA binding motifs. To control proteins without modifying them chemically or genetically, multivalent ligands and aptamers that reversibly inhibit their function provide valuable tools to regulate proteins in a noncovalent manner. The goal of this feature article is to give an overview of strategies developed to control protein activity via oligonucleotide-based triggers, as well as hurdles yet to be taken to obtain fully autonomous systems that interrogate, process and act on their environments by means of DNA-based protein control.

Fluorescence-based force/tension sensors: a novel tool to visualize mechanical forces in structural proteins in live cells

SIGNIFICANCE

Three signaling systems, chemical, electrical, and mechanical, ubiquitously contribute to cellular activities. There is limited information on the mechanical signaling system because of a lack of tools to measure stress in specific proteins. Although significant advances in methodologies such as atomic force microscopy and laser tweezers have achieved great success in single molecules and measuring the mean properties of cells and tissues, they cannot deal with specific proteins in live cells.

RECENT ADVANCES

To remedy the situation, we developed a family of genetically encoded optical force sensors to measure the stress in structural proteins in living cells. The sensors can be incorporated into specific proteins and are not harmful in transgenic animals. The chimeric proteins distribute and function as their wild-type counterparts, and local stress can be read out from changes in Förster resonance energy transfer (FRET).

CRITICAL ISSUES

Our original sensor used two mutant green fluorescence proteins linked by an alpha helix that served as a linking spring. Ever since, we have improved the probe design in a number of ways. For example, we replaced the helical linker with more common elastic protein domains to better match the compliance of the wild-type hosts. We greatly improved sensitivity by using the angular dependence of FRET rather than the distance dependence as the transduction mechanism, because that has nearly 100% efficiency at rest and nearly zero when stretched.

FUTURE DIRECTIONS

These probes enable researchers to investigate the roles of mechanical force in cellular activities at the level of single molecules, cells, tissues, and whole animals.

Critical bending torque of DNA is a materials parameter independent of local base sequence

Short double-stranded DNA molecules exhibit a softening transition under large bending which is quantitatively described by a critical bending torque τ_{c} at which the molecule develops a kink. Through equilibrium measurements of the elastic energy of short (∼10 nm), highly stressed DNA molecules with a nick at the center we determine τ_{c} for different sequences around the nick. We find that τ_{c} is a robust materials parameter essentially independent of sequence. The measurements also show that, at least for nicked DNA, the local structure at the origin of the softening transition is not a single-stranded "bubble."

DNA kinks and bubbles: temperature dependence of the elastic energy of sharply bent 10-nm-size DNA molecules

A 10-nm-long DNA molecule can bend through large angles reversibly. Past the linear regime, its equilibrium nonlinear bending elasticity is governed by a critical bending torque τ(c)≈30pN×nm at which the molecule develops a kink. This nonlinearity has long been attributed to the nucleation of a bubble or melted region in the molecule. Here we measure the temperature dependence of the critical bending torque for nicked DNA, and determine that the entropy associated with the kink in the nonlinear regime is negligible. Thus in the case of nicked DNA the kink is not a bubble, but a compact region deformed beyond a yield strain. We further argue that, with our boundary conditions, the same is likely true for intact DNA. The present measurements confirm that the critical bending torque τ(c) is a materials parameter of DNA mechanics analogous to the bending modulus B≈200pN×nm.

Orientation-based FRET sensor for real-time imaging of cellular forces

Mechanical stress is an unmapped source of free energy in cells. Mapping the stress fields in a heterogeneous time-dependent environment like that found in cells requires probes that are specific for different proteins and respond to biologically relevant forces with minimal disturbance to the host system. To meet these goals, we have designed a genetically encoded stress sensor with minimal volume and high sensitivity and dynamic range. The new FRET-based sensor, called cpstFRET, is designed to be modulated by the angles between the donor and acceptor rather than the distance between them. Relative to other probes, it is physically smaller and exhibits a greater dynamic range and sensitivity and expresses well. For in vivo testing, we measured stress gradients in time and space in non-erythroid spectrin in several different cell types and found that spectrin is under constitutive stress in some cells but not in others. Stresses appear to be generated by both F-actin and tubulin. The probe revealed, for the first time, that spectrin undergoes time-dependent force modulation during cell migration. cpstFRET can be employed in vitro, in vivo and in situ, and when incorporated into biologically expressed extracellular polymers such as collagen, it can report multidimensional stress fields.

Real Time FRET Based Detection of Mechanical Stress in Cytoskeletal and Extracellular Matrix Proteins

A molecular force sensing cassette (stFRET) was incorporated into actinin, filamin, and spectrin in vascular endothelial cells (BAECs) and into collagen-19 in Caenorhabditis elegans. To estimate the stress sensitivity of stFRET in solution, we used DNA springs. A 60-mer loop of single stranded DNA was covalently linked to the external cysteines of the donor and acceptor. When the complementary DNA was added it formed double stranded DNA with higher persistence length, stretching the linker and substantially reducing FRET efficiency. The probe stFRET detected constitutive stress in all cytoskeletal proteins tested, and in migrating cells the stress was greater at the leading edge than the trailing edge. The stress in actinin, filamin and spectrin could be reduced by releasing focal attachments from the substrate with trypsin. Inhibitors of actin polymerization produced a modest increase in stress on the three proteins suggesting they are mechanically in parallel. Local shear stress applied to the cell with a perfusion pipette showed gradients of stress leading from the site of perfusion. Transgenic C. elegans labeled in collagen-19 produced a behaviorally and anatomically normal animal with constitutive stress in the cuticle. Stretching the worm visibly stretched the probe in collagen showing that we can trace the distribution of mean tissue stress in specific molecules. stFRET is a general purpose dynamic sensor of mechanical stress that can be expressed intracellularly and extracellularly in isolated proteins, cells, tissues, organs and animals.

Elastic energy of protein-DNA chimeras

We present experimental measurements of the equilibrium elastic energy of protein-DNA chimeras, for two different sets of attachment points of the DNA "molecular spring" on the surface of the protein. Combining these with measurements of the enzyme's activity under stress and a mechanical model of the system, we determine how the elastic energy is partitioned between the DNA and the protein. The analysis shows that the protein is mechanically stiffer than the DNA spring.

Protein-DNA chimeras: synthesis of two-arm chimeras and non-mechanical effects of the DNA spring

DNA molecular springs have recently been used to control the activity of enzymes and ribozymes. In this approach, the mechanical stress exerted by the molecular spring alters the enzyme's conformation and thus the enzymatic activity. Here we describe a method alternative to our previous one to attach DNA molecular springs to proteins, where two separate DNA 'arms' are coupled to the protein and subsequently ligated. We report certain non-mechanical effects associated with the DNA spring observed in some chimeras with specific DNA sequences and the nucleotide binding enzyme guanylate kinase. If a ssDNA 'arm' is attached to the protein by one end only, we find that in some cases (depending on the DNA sequence and attachment point on the protein's surface) the unhybridized DNA arm inhibits the enzyme, while hybridization of the DNA arm leads to an apparent activation of the enzyme. One interpretation is that, in these cases, hybridization of the DNA arm removes it from the vicinity of the active site of the enzyme. We show how mechanical and non-mechanical effects of the DNA spring can be distinguished. This is important if one wants to use the protein-DNA chimeras to quantitatively study the response of the enzyme to mechanical perturbations.